[med-svn] [Git][med-team/pftools][master] 6 commits: Use Github tags instead of releases
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 25 09:16:57 GMT 2022
Andreas Tille pushed to branch master at Debian Med / pftools
Commits:
95486f8f by Andreas Tille at 2022-01-25T09:58:07+01:00
Use Github tags instead of releases
- - - - -
faba900e by Andreas Tille at 2022-01-25T09:58:29+01:00
routine-update: New upstream version
- - - - -
3ea320c1 by Andreas Tille at 2022-01-25T09:58:30+01:00
New upstream version 3.2.11
- - - - -
ea8c0564 by Andreas Tille at 2022-01-25T10:00:50+01:00
Update upstream source from tag 'upstream/3.2.11'
Update to upstream version '3.2.11'
with Debian dir d33db93b0ad677add8a637a11624b74f19587bd2
- - - - -
4a135234 by Andreas Tille at 2022-01-25T10:01:46+01:00
Add missing build dependency on dh addon.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
- - - - -
27db68c3 by Andreas Tille at 2022-01-25T10:05:45+01:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- .gitignore
- CMakeLists.txt
- Docker/README.docker
- README.md
- debian/changelog
- debian/control
- debian/watch
- src/C/config.h.cmake
- tests/examples/test_V3.sh.cmake
Changes:
=====================================
.gitignore
=====================================
@@ -1,4 +1,5 @@
build/
+testing/
\.kdev4/
=====================================
CMakeLists.txt
=====================================
@@ -1,10 +1,10 @@
#########################################################################################
# PfTools versioning
#
-SET(VERSION "3.2.8")
+SET(VERSION "3.2.11")
SET(MAJOR_VERSION "3")
SET(MINOR_VERSION "2")
-SET(PATCH_VERSION "8")
+SET(PATCH_VERSION "11")
SET(DATA_PATH "share/data" CACHE STRING "Installation data folder" )
SET(DOC_PATH "share/doc" CACHE STRING "Installation doc folder" )
SET(MAN1_PATH "share/man/man1" CACHE STRING "Installation man1 folder" )
@@ -396,7 +396,7 @@ ADD_SUBDIRECTORY(data)
#########################################################################################
# Enabling TESTING
include(CTest)
-SET(TESTS_DIRECTORY "${PROJECT_SOURCE_DIR}/Tests" CACHE PATH "Directory for tests")
+SET(TESTS_DIRECTORY "${PROJECT_SOURCE_DIR}/testing" CACHE PATH "Directory for tests")
SET(TESTS_DATA_DIR "${PROJECT_SOURCE_DIR}/tests")
IF (NOT EXISTS "${TESTS_DIRECTORY}" )
FILE(MAKE_DIRECTORY "${TESTS_DIRECTORY}" )
=====================================
Docker/README.docker
=====================================
@@ -1,5 +1,5 @@
# Build Docker image
-export PFTOOLS_VERSION=3.2.6
+export PFTOOLS_VERSION=3.2.11
docker build -t pftools:$PFTOOLS_VERSION --no-cache=true --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg PFTOOLS_VERSION=$PFTOOLS_VERSION -f Dockerfile . 2>&1 >pftools.Dockerfile.log
=====================================
README.md
=====================================
@@ -1,4 +1,24 @@
-# PfTools v3.2
+[](http://bioconda.github.io/recipes/pftools/README.html)
+[](https://anaconda.org/bioconda/pftools)
+[](https://anaconda.org/bioconda/pftools)
+
+PfTools
+=========================================
+
+## Table of Contents
+
+ * [Foreword](#foreword)
+ * [Installation](#installation)
+ * [Using Docker](#using-docker)
+ * [Using Singularity](#using-singularity)
+ * [Bioconda](#bioconda)
+ * [Manually](#manually)
+ * [Generalized profile syntax](#generalized-profile-syntax)
+ * [Algorithms description](#algorithms-description)
+ * [Applications of the Pftools](#applications-of-the-pftools)
+ * [Authors](#authors)
+
+# Foreword
(C) Copyright SIB Swiss Institute of Bioinformatics
available from https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.
@@ -7,9 +27,86 @@ available from https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.
Version 3 contains the original FORTRAN 77 pftools (release 2.3)
and the new pftoolsV3 programs.
-The 'pftools' package documententation is unfortunately scattered over many
-different places. Here is an annotated list of the relevant documents we are
-aware of:
+# Installation
+
+### Using Docker
+
+First you must have [Docker](https://docs.docker.com/get-docker/) installed and running.
+Secondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).
+Then:
+ ```
+# get the chosen pftools container version
+docker pull quay.io/biocontainers/pftools:2.3.5--h4333106_0
+ or
+docker pull sibswiss/pftools:3.2.8
+# use an pftools's tool e.g. pfscan
+docker run quay.io/biocontainers/pftools:2.3.5--h4333106_0 pfscan -h
+ or
+docker run sibswiss/pftools:3.2.8 pfscan -h
+ ```
+
+### Using Singularity
+
+First you must have [Singularity](https://sylabs.io/guides/master/user-guide/quick_start.html) installed and running.
+Secondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).
+Then:
+```
+# get the chosen pftools container version
+singularity pull docker://quay.io/biocontainers/quay.io/biocontainers/pftools:2.3.5--h4333106_0
+ or
+singularity pull docker://sibswiss/pftools:3.2.8
+# run the container
+singularity run pftools_2.3.5--h4333106_0.sif
+```
+
+You are now in the container. You can use an pftools's tool e.g. pfscan doing
+```
+pfscan -h
+```
+
+## Bioconda
+
+```
+conda install -c bioconda pftools
+```
+
+## Manually
+
+See [here](./INSTALL) for more information
+
+**Prerequisite**
+
+ * cmake >= 3.7
+ * gcc >= 4.6
+ * gfortran (or g77 or f77) for release 2.3 source code
+ * perl >= 5.5.3
+ * File::Slurp
+
+**BUILD**
+```
+git clone https://github.com/sib-swiss/pftools3.git
+cd pftools3
+mkdir build
+cd build/
+cmake ..
+```
+
+**COMPILE**
+```
+make
+```
+
+**INSTALL**
+```
+make install
+```
+
+**CHECK/TEST**
+```
+make test
+```
+
+After installation, in the share/examples/ subdirectory, the *test_V3.sh* shell script is a good starting point for using pfsearchV3/pfscanV3.
# Generalized profile syntax
@@ -27,10 +124,6 @@ it was originally published in
PubMed PMID: [7584418](https://www.ncbi.nlm.nih.gov/pubmed/7584418).
-# Command-line tutorial
-
-After installation, in the share/examples/ subdirectory, the *test_V3.sh* shell script is a good starting point for using pfsearchV3/pfscanV3.
-
# Algorithms description
Technical details about how profiles can be constructed and parametrized
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+pftools (3.2.11-1) unstable; urgency=medium
+
+ * Use Github tags instead of releases
+ * New upstream version
+ * Add missing build dependency on dh addon.
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jan 2022 10:01:51 +0100
+
pftools (3.2.8-1) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -9,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),
libfile-slurp-perl,
libbz2-dev,
libreadline-dev,
- zlib1g-dev
+ zlib1g-dev,
+ debhelper
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/pftools
Vcs-Git: https://salsa.debian.org/med-team/pftools.git
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s%(?:.*?)?v(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/sib-swiss/pftools3//releases .*/v?@ANY_VERSION@\.tar\.gz
+ https://github.com/sib-swiss/pftools3/tags .*/v?@ANY_VERSION@\.tar\.gz
=====================================
src/C/config.h.cmake
=====================================
@@ -10,11 +10,9 @@
#define __USE_WINAPI__
#endif
-#cmakedefine USE_AFFINITY
-#if defined(USE_AFFINITY)
-# if defined(__GNUC__) && !defined(USE_WINAPI)
-# define _GNU_SOURCE
-# endif
+/* NOTE Compilation fails if _GNU_SOURCE is not defined with affinity off */
+#if defined(__GNUC__) && !defined(USE_WINAPI)
+# define _GNU_SOURCE
#endif
/*
=====================================
tests/examples/test_V3.sh.cmake
=====================================
@@ -127,11 +127,11 @@ $PFSCANV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ
#
# Default output mode:
#----------------------------------------------------------------------#
-$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit
+$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit
$PFSEARCHV3 -n -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.3.hit
diff -b $TMPDIR/sh3.VAV_HUMAN.2.hit $TMPDIR/sh3.VAV_HUMAN.3.hit # expecting no difference
-$PFSEARCH -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit
+$PFSEARCH -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit
$PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.3.hit
diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit # expecting no difference
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12
--
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12
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